Whole genome sequencing used to investigate Salmonella outbreak

The U.S. Centers for Disease Control and Prevention (CDC), and the Food and Drug Administration (FDA), recently released a report on a 2016 Salmonella outbreak, identifying it to the public for the first time.

More than 30 people across nine U.S. states were sickened. Eight of those people were hospitalized, with victims spreading from Texas to Minnesota, between May 6 and July 9.

The outbreak was traced back to fresh hot peppers.

“Investigators could not determine what specific type of hot pepper was causing illness, or which farm was producing the peppers,” a spokesperson told Food Safety News. “Due to the short shelf-life of fresh peppers, the contaminated peppers were most likely no longer being sold or served when investigators suspected peppers as the outbreak source.”

Why are consumers only just now hearing about the outbreak? There just wasn’t any information that was useful by the time the FDA and the CDC realized what was going on.

“The FDA worked with the CDC on this outbreak, however, the traceback investigation was unable to uncover a common source for the peppers at the time, and therefore we did not have any actionable information to share with consumers,” said another spokesperson.

During the investigation, researchers used whole genome sequencing (WGS), among other techniques, to get a clearer picture of the situation. WGS reveals the entire DNA structure of an organism, which in this case, allowed researchers to identify the particular variation of Salmonella. They then attempted to trace where the bacteria came from by seeking the particular variant in other foods or food production sites. WGS can identify some strains of Salmonella that traditional methods, like pulsed-field gel electrophoresis, cannot.

The report further highlighted the difficulties of investigating peppers:

“Both the complexity of the hot pepper supply chain, as well as the difficulties of identifying specific pepper types through epidemiologic investigations create challenges to investigating outbreaks linked to fresh hot peppers.”

Like many fresh fruits and vegetables, peppers carry a pathogen risk thanks to their close contact with water, soil and equipment before and after being harvested.

The FDA is currently paying special attention to peppers and cucumbers, which have been attributed to numerous outbreaks and recalls in recent years. Two people were killed and approximately 1,500 made sick in 2008 due to an outbreak stemming from fresh hot peppers.

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